MC3T3 osteoblast-like cells cultured at alkaline pH: Microarray data (Affymetrix GeneChip Mouse 2.0 ST)
It is well known that pH plays a pivotal role in the control of bone remodeling. However, no comprehensive gene expression data are available for the effects of alkaline pH on osteoblasts. We cultured differentiating MC3T3-E1 osteoblast-like cells at pH 7.4, 7.8, and 8.4 for 14 days. To identify dif...
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| Format: | Article |
| Language: | English |
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Elsevier
2017-08-01
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| Series: | Data in Brief |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340917302044 |
| _version_ | 1818924405800042496 |
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| author | Anne-Marie Galow Alexander Rebl Dirk Koczan Jan Gimsa |
| author_facet | Anne-Marie Galow Alexander Rebl Dirk Koczan Jan Gimsa |
| author_sort | Anne-Marie Galow |
| collection | DOAJ |
| description | It is well known that pH plays a pivotal role in the control of bone remodeling. However, no comprehensive gene expression data are available for the effects of alkaline pH on osteoblasts. We cultured differentiating MC3T3-E1 osteoblast-like cells at pH 7.4, 7.8, and 8.4 for 14 days. To identify differential gene expression, microarray data were collected with Affymetrix GeneChips. The data were validated by real-time PCRs for five genes that were found to be greatly regulated in the GeneChip-experiments (DMP1, FABP4, SFRP2 and TNFRSF19) or considered relevant for the terminal function of osteoblasts (DMP1 and ATF4). All the data are available from the Gene Expression Omnibus database (GEO accession: GSE84907). Here, we provide pathway analyses of known protein coding genes that were down-regulated or up-regulated by greater than 2.0-fold. The regulation datasets obtained from comparisons of pH 7.8 and 7.4, as well as pH 8.4 and 7.4 share a high number of differentially expressed genes. When comparing pH 8.4 and 7.8, other genes mainly emerge, suggesting not only a simple amplification of the effects at pH 8.4 that were already induced at pH 7.8 but also the induction of different pathways. For a more detailed analysis, different mammalian functional gene networks were assigned to each dataset. After merging and manual optimization of the network graphs, three combined functional gene networks were obtained that reflected distinct pH-dependent cellular responses. A common feature of the networks was the central role of p38 MAP kinase. The microarray data presented here are related to the research article doi:10.1016/j.bbrep.2017.02.001 (Galow et al., 2017) [1]. Keywords: Bone, Gene regulation, Functional gene networks, p38 MAPK, Murine cell line, Quantitative real-time PCR, Robust Multi-Array Average, Fold change bias, Differential gene expression, Ingenuity Pathway Analyses |
| first_indexed | 2024-12-20T02:24:49Z |
| format | Article |
| id | doaj.art-740a1d0743254c1f859f5b2f581b38aa |
| institution | Directory Open Access Journal |
| issn | 2352-3409 |
| language | English |
| last_indexed | 2024-12-20T02:24:49Z |
| publishDate | 2017-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj.art-740a1d0743254c1f859f5b2f581b38aa2022-12-21T19:56:44ZengElsevierData in Brief2352-34092017-08-0113108114MC3T3 osteoblast-like cells cultured at alkaline pH: Microarray data (Affymetrix GeneChip Mouse 2.0 ST)Anne-Marie Galow0Alexander Rebl1Dirk Koczan2Jan Gimsa3University of Rostock, Gertrudenstr. 11a, 18057 Rostock, GermanyInstitute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, GermanyInstitute of Immunology, University of Rostock, Schillingallee 70, 18055 Rostock, GermanyUniversity of Rostock, Gertrudenstr. 11a, 18057 Rostock, Germany; Corresponding author.It is well known that pH plays a pivotal role in the control of bone remodeling. However, no comprehensive gene expression data are available for the effects of alkaline pH on osteoblasts. We cultured differentiating MC3T3-E1 osteoblast-like cells at pH 7.4, 7.8, and 8.4 for 14 days. To identify differential gene expression, microarray data were collected with Affymetrix GeneChips. The data were validated by real-time PCRs for five genes that were found to be greatly regulated in the GeneChip-experiments (DMP1, FABP4, SFRP2 and TNFRSF19) or considered relevant for the terminal function of osteoblasts (DMP1 and ATF4). All the data are available from the Gene Expression Omnibus database (GEO accession: GSE84907). Here, we provide pathway analyses of known protein coding genes that were down-regulated or up-regulated by greater than 2.0-fold. The regulation datasets obtained from comparisons of pH 7.8 and 7.4, as well as pH 8.4 and 7.4 share a high number of differentially expressed genes. When comparing pH 8.4 and 7.8, other genes mainly emerge, suggesting not only a simple amplification of the effects at pH 8.4 that were already induced at pH 7.8 but also the induction of different pathways. For a more detailed analysis, different mammalian functional gene networks were assigned to each dataset. After merging and manual optimization of the network graphs, three combined functional gene networks were obtained that reflected distinct pH-dependent cellular responses. A common feature of the networks was the central role of p38 MAP kinase. The microarray data presented here are related to the research article doi:10.1016/j.bbrep.2017.02.001 (Galow et al., 2017) [1]. Keywords: Bone, Gene regulation, Functional gene networks, p38 MAPK, Murine cell line, Quantitative real-time PCR, Robust Multi-Array Average, Fold change bias, Differential gene expression, Ingenuity Pathway Analyseshttp://www.sciencedirect.com/science/article/pii/S2352340917302044 |
| spellingShingle | Anne-Marie Galow Alexander Rebl Dirk Koczan Jan Gimsa MC3T3 osteoblast-like cells cultured at alkaline pH: Microarray data (Affymetrix GeneChip Mouse 2.0 ST) Data in Brief |
| title | MC3T3 osteoblast-like cells cultured at alkaline pH: Microarray data (Affymetrix GeneChip Mouse 2.0 ST) |
| title_full | MC3T3 osteoblast-like cells cultured at alkaline pH: Microarray data (Affymetrix GeneChip Mouse 2.0 ST) |
| title_fullStr | MC3T3 osteoblast-like cells cultured at alkaline pH: Microarray data (Affymetrix GeneChip Mouse 2.0 ST) |
| title_full_unstemmed | MC3T3 osteoblast-like cells cultured at alkaline pH: Microarray data (Affymetrix GeneChip Mouse 2.0 ST) |
| title_short | MC3T3 osteoblast-like cells cultured at alkaline pH: Microarray data (Affymetrix GeneChip Mouse 2.0 ST) |
| title_sort | mc3t3 osteoblast like cells cultured at alkaline ph microarray data affymetrix genechip mouse 2 0 st |
| url | http://www.sciencedirect.com/science/article/pii/S2352340917302044 |
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